Notes from the life of a computational biologist

Daily Archives: August 11, 2006

I’m about a month behind the times on this, but EMBOSS 4.0.0 has been released. Major EMBOSS releases occur traditionally on St. Swithin’s Day, July 15th (how charmingly English!)
I’ve long been a fan of EMBOSS – it’s a great suite of small but useful tools and it integrates well with BioPerl. It’s a toolbox, in the *NIX tradition. It’s also a great example of a tool that many less computer literate biologists are completely unaware of, simply through their fear of the command line.

The changelog is an interesting read this year. Amongst other things, IUPAC have now designated ‘O’ the symbol for pyrrolysine. This means that any alphabetical character is now valid in a protein sequence (B=D/N, J=I/L, O=pyrrolysine, U=selenocysteine, X=unknown, Z=E/Q). It’ll be interesting to see how long it takes for that to be properly represented in all databases and software.